INNER CODE UNIT · Rust

bio_aligner

soedinglab/metaeuk · lib/mmseqs/lib/block-aligner/benches/rand_scan.rs:26

        let mut bio_aligner = Aligner::with_capacity(q.len(), r.len(), -10, -1, &blosum62);
        bio_aligner.global(&q, &r).score
    });
}

#[cfg(not(any(feature = "simd_wasm", feature = "simd_neon")))]
fn bench_parasailors_aa_core<const K: usize>(b: &mut Bencher, len: usize) {
    let mut rng = StdRng::seed_from_u64(1234);
    let r = black_box(rand_str(len, &AMINO_ACIDS, &mut rng));
    let q = black_box(rand_mutate(&r, K, &AMINO_ACIDS, &mut rng));
    let matrix = Matrix::new(MatrixType::Blosum62);
    let profile = parasailors::Profile::new(&q, &matrix);

    b.iter(|| {
        global_alignment_score(&profile, &r, 11, 1)
    });
}

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